Two goals in the space of four second-half minutes were enough to claim all three points.
The first was a stunning drive from Geovanni and then Daniel Cousin powerfully headed home from a corner.
Arsenal's goal was also scored by a Hull player, Paul McShane, whose inadvertent misdemeanor was forgotten well before full-time.
Arsenal were looking to reclaim top spot in the Premier League with a win over the Tigers - the late kick-off and a Chelsea win had relegated the Gunners to fourth place - but they failed miserably.
The Gunners were looking to take a quick advantage, but Hull looked solid in the early exchanges limiting the home side to just a couple of tame efforts.
First came a header from Kolo Toure before a shot which was dragged wide by Cesc Fabregas.
The Gunners did have the ball in the net on 15 minutes, but Emmanuel Adebayor was adjudged to have fouled Michael Turner prior to heading the ball home and the strike was chalked off.
That did spur the home side on as did Phil Brown's side's attempts at physical intimidation.
The tackles were flying in and referee Alan Wiley was clearly in for a busy evening, but the Gunners were also guilty of leaving a foot in too.
George Boateng had a 25-yard effort blocked by Fabregas, who sent the ball looping over his own bar.
It was the Gunners though who took the lead on 51 minutes even though the ball was put into the net by a Hull player.
Theo Walcott was continuing to make a nuisance of himself on the right side of the area and got to the byline to pull the ball back for Adebayor.
The ball bounced of the striker's shin across goal but was turned in by McShane, who slid in to deny Fabregas the opportunity.
Hull's heads did not drop though and former Spurs man Dean Marney forced Manuel Almunia into a save with an overhead kick from inside the area in the 56th minute.
The Hull fans were in raptures in the 62nd minute when Geovanni, in acres of space, hit a looping 25-yarder past the outstretched Almunia to level the scores.
They were in dreamland four minutes later when Cousin rose highest to power home Andy Dawson's corner into the top left corner for Hull to take a stunning lead.
Hull then pulled most of their players back in an effort to hold onto the lead.
The Gunners brought on midweek hat-trick hero Carlos Vela in an effort to give them a sharper cutting edge.
Robin van Persie should have done better in the 82nd minute when put through by Fabregas, but pulled his right-footed shot across goal and wide of the left post.
As injury time ticked away, Boaz Myhill pulled off a magnificent save from Fabregas' 25-yard drive to keep his side in charge of all three points.
The home fans poured out before the whistle, many missing van Persie's shot that shaved the top of the bar with Myhill well beaten.
That was the last real effort for the Gunners, who lost their second game of the season and their first at the Emirates for over 17 months.